TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets.

TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X's predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user's web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researchers can use to better illuminate understudied proteins.

Ablative Radiation Therapy to Restrain Everything Safely Treatable (ARREST): A Phase 1 Study of Stereotactic Ablative Radiation Therapy for Polymetastatic Disease.

PURPOSE: This phase 1 study aimed to assess the safety and feasibility of SABR therapy delivery to all sites of polymetastatic disease (>10 metastases). METHODS AND MATERIALS: A 3 + 3 study design was used with 5 dose levels from 6 Gy (6 Gy × 1) to 30 Gy (6 Gy weekly × 5). Dose-limiting toxicity (DLT) was defined as any grade 4 or 5 toxicity or more than 3 grade 3 toxicities within 6 weeks of treatment. The primary endpoint was the maximal tolerated dose, defined as the dose level where ≥2/6 of patients experienced DLT. Secondary endpoints included quality of life (Functional Assessment of Cancer Therapy - General and European Quality of Life 5 Dimension 5 Level) at 6 weeks posttreatment, progression-free survival, and overall survival. RESULTS: Thirteen patients were accrued: 12 Gy (n = 3), 18 Gy (n = 3), 24 Gy (n = 4), and 30 Gy (n = 3), and 207 lesions were treated. Nine patients (69%) had acute toxicity: grade 1 (n = 6, 46%), grade 2 (n = 2, 15%; n = 1 pneumonitis and n = 1 fatigue), and grade 3 (n = 1, 7.7% neutropenia). There were no grade 4 or 5 toxicities. Mean ± SD quality of life (Functional Assessment of Cancer Therapy - General and European Quality of Life 5 Dimension 5 Level health state) was 80.4 ± 21.9 and 77.4 ± 20.9 at baseline versus 76.4 ± 21.8 and 68.0 ± 24.2 at 6-week follow-up, respectively (p = .009 and p = .055, respectively). With a median follow-up of 8.7 months posttreatment (IQR, 2.4-24 months), 8 of 13 patients had disease progression (62%). The median and 12-month progression-free survival were 3.6 months and 11.3%, respectively. The median and 12-month overall survival were 13.8 months and 62%, respectively. CONCLUSIONS: In this phase 1 trial, SABR therapy for polymetastatic disease was technically feasible with acceptable acute toxicity at dose levels up to 30 Gy (6 Gy weekly × 5). DLT was not observed.

In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.

To facilitate the detection and management of potential clinical antiviral resistance, in vitro selection of drug-resistant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) against the virus Mpro inhibitor nirmatrelvir (Paxlovid active component) was conducted. Six Mpro mutation patterns containing T304I alone or in combination with T21I, L50F, T135I, S144A, or A173V emerged, with A173V+T304I and T21I+S144A+T304I mutations showing >20-fold resistance each. Biochemical analyses indicated inhibition constant shifts aligned to antiviral results, with S144A and A173V each markedly reducing nirmatrelvir inhibition and Mpro activity. SARS-CoV-2 surveillance revealed that in vitro resistance-associated mutations from our studies and those reported in the literature were rarely detected in the Global Initiative on Sharing All Influenza Data database. In the Paxlovid Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients trial, E166V was the only emergent resistance mutation, observed in three Paxlovid-treated patients, none of whom experienced COVID-19-related hospitalization or death.

Aortic tissue stiffness and tensile strength are correlated with density changes following proteolytic treatment.

INTRODUCTION: Dissection or rupture of the aorta is accompanied by high mortality rates, and there is a pressing need for better prediction of these events for improved patient management and clinical outcomes. Biomechanically, these events represent a situation wherein the locally acting wall stress exceed the local tissue strength. Based on recent reports for polymers, we hypothesized that aortic tissue failure strength and stiffness are directly associated with tissue mass density. The objective of this work was to test this novel hypothesis for porcine thoracic aorta. METHODS: Three tissue specimens from freshly harvested porcine thoracic aorta were treated with either collagenase or elastase to selectively degrade structural proteins in the tissue, or with phosphate buffer saline (control). The tissue mass and volume of each specimen were measured before and after treatment to allow for density calculation, then mechanically tested to failure under uniaxial extension. RESULTS: Protease treatments resulted in statistically significant tissue density reduction (sham vs. collagenase p = 0.02 and sham vs elastase p = 0.003), which in turn was significantly and directly correlated with both ultimate tensile strength (sham vs. collagenase p = 0.02 and sham vs elastase p = 0.03) and tangent modulus (sham vs. collagenase p = 0.007 and sham vs elastase p = 0.03). CONCLUSIONS: This work demonstrates for the first time that tissue stiffness and tensile strength are directly correlated with tissue density in proteolytically-treated aorta. These findings constitute an important step towards understanding aortic tissue failure mechanisms and could potentially be leveraged for non-invasive aortic strength assessment through density measurements, which could have implications to clinical care.

Refined step-by-step narrative review of robotic radical nephroureterectomy in the management of upper tract urothelial carcinoma.

Background and Objective: Upper tract urothelial carcinoma (UTUC) is a challenging clinical entity to diagnose and manage. Recent advances in robotic technology have permitted optimization of surgical technique in robot-assisted radical nephroureterectomy with bladder cuff excision (RNU/BCE), regional lymphadenectomy, and intra or perioperative instillation of intravesical chemotherapy. This has optimized the management of bulky upper tract disease and high-grade disease not amenable to segmental ureterectomy or nephron-sparing surgery. The purpose of this article is to highlight and review the surgical technique if RNU/BCE and regional lymphadenectomy utilized in our high-volume clinical practice. Methods: A review of our surgical approach was summarized for this narrative article. This technique has been refined over a course of more than 150 cases and 12 years of local experience with the procedure, as well as through multiple da Vinci® robotic surgical systems over the years. Key Content and Findings: RNU/BCE, regional template-based lymphadenectomy, and intra or perioperative instillation of intravesical chemotherapy is technically feasible and the procedure has been optimized via multiple iterations with a decade of local experience. The appropriate steps are outlined in this review. Conclusions: RNU/BCE, regional template-based lymphadenectomy, and intra or perioperative instillation of intravesical chemotherapy provides a refined, standardized, efficient approach for management of UTUC in appropriately selected patients. This surgical technique has also been undertaken in elderly patients including those with advanced age (>80 years old) with significant medical co-morbidities due to imperative, symptomatic indications. Further, this approach may be facilely adapted by urologists familiar with all forms of robotic renal surgery.

Adoption of robot-assisted radical nephroureterectomy permits a minimally invasive option for management of upper tract urothelial carcinoma in geriatric patients: comparison with non-geriatric patients with intermediate-term oncologic follow-up.

To assess the oncologic efficacy and safety of robot-assisted approach to radical nephroureterectomy (RARNU) in geriatric versus younger patients with upper tract urothelial carcinoma (UTUC). A single-center, retrospective cohort study was conducted from 2009 to 2022 of 145 patients (two cohorts: < 75 and ≥ 75 years old) with non-metastatic UTUC who underwent RARNU. Primary endpoint was UTUC-related recurrence of disease during surveillance (bladder-specific and metastatic). Safety was assessed according to 30-day, modified Clavien-Dindo (CD) classifications (Major: C.D. III-V). Survival estimates were performed using Kaplan-Meier method. There were 89 patients < 75 years (median 65 years) and 56 patients ≥ 75 years (median 81 years). Comparing the young versus geriatric cohorts: median follow-up 38 vs 24 months (p = 0.03, respectively) with similar 3-year bladder-specific recurrence survival (60% vs 67%, HR 0.70, 95% CI [0.35, 1.40], p = 0.31) and metastasis-free survival (79% vs 70%, HR 0.71, 95% CI [0.30, 1.70], p = 0.44). Expectedly, the younger cohort had a significant deviation in overall survival compared to the geriatric cohort at 1-year (89% vs 76%) and 3-years (72% vs 41%; HR 3.29, 95% CI [1.88, 5.78], p < 0.01). The 30-day major (1% vs 0) and minor complications (8% vs 14%, p = 0.87). Limitations include retrospective study design of a high-volume, single-surgeon experience. Compared to younger patients with UTUC, geriatric patients undergoing RARNU have similar oncologic outcomes at intermediate-term follow-up with no increased risk of 30-day perioperative complications. Thus, age alone should not be used to disqualify patients from definitive surgical management of UTUC with RARNU.

Harnessing the 1,3-azadiene-anhydride reaction for the regioselective and stereocontrolled synthesis of lactam-fused bromotetrahydropyrans by bromoetherification of lactam-tethered trisubstituted tertiary alkenols.

Halo-cycloetherification of lactam-tethered alkenols enables the construction of oxygen-heterocycles that are fused to nitrogen heterocycles via intramolecular halonium-induced nucleophilic addition. Specifically, tetrahydropyrans (THPs) that are fused to a nitrogen heterocycle constitute the core of several bioactive molecules, including tachykinin receptor antagonists and alpha-1 adrenergic antagonists. Although the literature is replete with successful examples of the halo-cycloetherification of simple mono- or disubstituted primary alkenols, methods for the modular, efficient, regioselective, and stereocontrolled intramolecular haloetherification of sterically encumbered trisubstituted tertiary alkenols are rare. Here, we describe a simple intramolecular bromoetherification strategy that meets these benchmarks and proceeds with exclusive 6-endo regioselectivity. The transformation employs mild and water-tolerant conditions, which bodes well for late-stage diversification. The hindered ethers contain four contiguous stereocenters as well as one halogen-bearing tetrasubstituted stereocenter.

Heparin-Induced Thrombocytopenia (HIT) in the Direct Oral Anticoagulants (DOAC) Era.

BACKGROUND: Heparin-induced thrombocytopenia (HIT) is an uncommon complication of heparin therapy with significant risk for severe morbidity and mortality. We investigated the role and outcome of direct oral anticoagulants (DOACs) for the management of HIT. METHODS: After institutional review board (IRB) approval, a retrospective review was performed identifying all patients with positive HIT serotonin-release assays between 2020 and 2022 at two hospitals. The demographic and clinical variables were collected as follows: initial anticoagulant, dosing and indication, interval before onset of HIT, thrombotic complications, platelet nadir and recovery, direct thrombin inhibitor (DTI) and DOAC usage, and clinical outcomes. RESULTS: 15 patients were included in the study. 8 underwent a vascular procedure, 3 had cardiac surgery, 1 patient had both and was included in both groups, and 5 patients had either noncardiac, nonvascular surgery, or no surgery. 14 patients received unfractionated heparin (93% with therapeutic dosing), and 1 received prophylactic enoxaparin prior to diagnosis of HIT. The average time to diagnosis of HIT was 10.77 days after initial anticoagulation. In-hospital mortality was 27%, related to Covid-19 infection (3/4) and intracranial hemorrhage (1/4). 40% developed thrombosis (67% venous, 33% arterial) after the diagnosis of HIT. 8/11 survivors were discharged on a DOAC. With DOAC therapy, platelet counts rebounded to an average of 265K ( ± 104.6 K) within an average of 2.3 days and 364K ( ± 273.9 K) within 30 days after initiation of a DOAC. No recurrent thrombosis occurred after DOAC administration and only one patient had persistent thrombocytopenia within 30 days. CONCLUSIONS: Mortality and thrombosis (arterial and venous) are common complications in patients diagnosed with HIT. In patients who survive to discharge, DOACs are the most common discharge antithrombotic agent, with low rates of recurrent thrombosis and thrombocytopenia.

INVESTIGATING THE RELATIONSHIP BETWEEN BLEEDING, CLOTTING, AND COAGULOPATHY DURING AUTOMATED PARTIAL REBOA STRATEGIES IN A HIGHLY LETHAL PORCINE HEMORRHAGE MODEL.

ABSTRACT: Background: Death due to hemorrhagic shock, particularly, noncompressible truncal hemorrhage, remains one of the leading causes of potentially preventable deaths. Automated partial and intermittent resuscitative endovascular balloon occlusion of the aorta (i.e., pREBOA and iREBOA, respectively) are lifesaving endovascular strategies aimed to achieve quick hemostatic control while mitigating distal ischemia. In iREBOA, the balloon is titrated from full occlusion to no occlusion intermittently, whereas in pREBOA, a partial occlusion is maintained. Therefore, these two interventions impose different hemodynamic conditions, which may impact coagulation and the endothelial glycocalyx layer. In this study, we aimed to characterize the clotting kinetics and coagulopathy associated with iREBOA and pREBOA, using thromboelastography (TEG). We hypothesized that iREBOA would be associated with a more hypercoagulopathic response compared with pREBOA due to more oscillatory flow. Methods: Yorkshire swine (n = 8/group) were subjected to an uncontrolled hemorrhage by liver transection, followed by 90 min of automated pREBOA, iREBOA, or no balloon support (control). Hemodynamic parameters were continuously recorded, and blood samples were serially collected during the experiment (i.e., eight key time points: baseline (BL), T0, T10, T30, T60, T90, T120, T210 min). Citrated kaolin heparinase assays were run on a TEG 5000 (Haemonetics, Niles, IL). General linear mixed models were employed to compare differences in TEG parameters between groups and over time using STATA (v17; College Station, TX), while adjusting for sex and weight. Results: As expected, iREBOA was associated with more oscillations in proximal pressure (and greater magnitudes of peak pressure) because of the intermittent periods of full aortic occlusion and complete balloon deflation, compared to pREBOA. Despite these differences in acute hemodynamics, there were no significant differences in any of the TEG parameters between the iREBOA and pREBOA groups. However, animals in both groups experienced a significant reduction in clotting times (R time: P < 0.001; K time: P < 0.001) and clot strength (MA: P = 0.01; G: P = 0.02) over the duration of the experiment. Conclusions: Despite observing acute differences in peak proximal pressures between the iREBOA and pREBOA groups, we did not observe any significant differences in TEG parameters between iREBOA and pREBOA. The changes in TEG profiles were significant over time, indicating that a severe hemorrhage followed by both pREBOA and iREBOA can result in faster clotting reaction times (i.e., R times). Nevertheless, when considering the significant reduction in transfusion requirements and more stable hemodynamic response in the pREBOA group, there may be some evidence favoring pREBOA usage over iREBOA.

Investigating the Effects of Discrimination Experiences on Everyday Metamemory Accuracy.

OBJECTIVES: Lifetime and daily experiences of discrimination contribute to impaired performance on cognitive assessments. However, the underlying mechanism by which discrimination negatively affects cognition is unclear. Recent research investigating stress-induced impairment of metamemory may address the relationship between discrimination experiences and cognitive impairment. METHODS: The aim of this study was to determine the relationship of lifetime and daily experiences of discrimination, daily affect balance, baseline objective cognitive performance, and sociodemographic variables (age, race, ethnicity, and sex) with metamemory accuracy across the lifespan (ages 20-75). Impaired metamemory accuracy was defined by the number of subjective cognitive complaints. Diary data from the Midlife in the United States (MIDUS Refresher 1) Daily Diary Project (N = 782) was used for these analyses. RESULTS: Results from linear mixed model analyses showed significant within-person effects of daily discrimination, where people who reported more daily discrimination also reported lower metamemory accuracy, and daily affect balance, where people who reported very negative affect also reported lower metamemory accuracy. Additionally, linear mixed model analyses revealed significant between-person effects of race on metamemory accuracy, with individuals from minoritized racial groups generally reporting poorer metamemory accuracy. Daily discrimination experiences also interacted with other variables in predicting day-to-day metamemory accuracy. DISCUSSION: These findings add to our understanding of how psychosocial stress in the form of daily discrimination experiences may impair metamemory processes contributing to increased subjective cognitive complaints. Future research should consider the contribution of daily experiences of discrimination across the lifespan to poor cognitive outcomes in later life.

Revisiting the 1,3-azadiene-succinic anhydride annulation reaction for the stereocontrolled synthesis of allylic 2-oxopyrrolidines bearing up to four contiguous stereocenters.

Polysubstituted 2-oxopyrrolidines bearing at least two contiguous stereocenters constitute the core of several pharmaceuticals, including clausenamide (antidementia). Here, we describe a flexible annulation strategy, which unites succinic anhydride and 1,3-azadienes to produce allylic 2-oxopyrrolidines bearing contiguous stereocenters. The approach is chemoselective, efficient, modular, scalable, and diastereoselective. The scalable nature of the reactions offers the opportunity for post-diversification, leading to incorporation of motifs with either known pharmaceutical value or that permit subsequent conversion to medicinally relevant entities.

The impact of Covid-19 pandemic on the research portfolio and approval turnaround time at the Kenya Medical Research Institute.

BACKGROUND: The Covid-19 pandemic led to an unprecedented impact on many sectors globally including research. We assessed the impact of the Covid-19 pandemic on the research portfolio, and on the approval turnaround time for research protocols submitted to the Scientific and Ethics Review Unit (SERU), at the Kenya Medical Research Institute (KEMRI). METHODS: We compared research protocols submitted between October 01, 2019 and March 31, 2020 (Period 1), to those submitted between April 1 and September 30, 2020 (Period 2). A document review tool was used to extract data from the 198 research protocols reviewed and approved over the two periods. RESULTS: In the two periods under review, the single largest percentage of protocols (89/198, 45.4%) involved infectious and parasitic diseases, and the single largest percentage of study designs was cross-sectional (75/198, 38%). Before the pandemic, the median time taken to review KEMRI-linked protocols was 87 days and for non-KEMRI linked protocols it was 121 days. During the pandemic, approval turnaround time dropped for both KEMRI and non-KEMRI protocols to 66 days and 92 days, respectively, due to the streamlined processes at the KEMRI SERU. CONCLUSION: The research portfolio was minimally affected by the pandemic. The adoption of email submission, and faster-than-usual processing and review protocols during the pandemic reduced the approval turnaround time.

The impact of expanded access programs for systemic anticancer therapy in an Irish cancer centre.

BACKGROUND: Expanded access programs (EAPs) allow cancer patients with unmet clinical need to obtain access to pre-authorisation treatments. There is no standardised process for implementing these programs nationally, and real-world data on their impact is lacking. AIMS: This study aimed to evaluate the prevalence of such EAPs and their impact in a cancer centre. METHODS: Data relating to adult cancer patients treated via EAPs from 2011 to 2021 in three Cork university hospitals was collated. Descriptive statistics were employed to get an overview of the impact these programs currently have on cancer care provision. RESULTS: We identified 193 patients who accessed EAPs during the study period, availing of 33 separate drugs for a total of 50 different cancer indications. The prevalence of EAP usage was shown to have been trending upwards in recent years with a total of 189 programs being accessed throughout the period. Drugs provided were from a number of different anti-cancer drug classes, particularly targeted therapies (n = 18) and immune checkpoint inhibitors (n = 17). Cancers from a wide range of both solid and liquid tumour types were treated with EAP drugs, and patients treated were from across a broad spectrum of ages (26-82, SD 11.99). CONCLUSIONS: EAPs have an increasing role in accessing novel cancer therapies in our community and by extension nationally. Equity of EAP access would be facilitated by a national registry of available agents which we have established. Assessment of their benefits and toxicities would be enhanced by the requirement for a real-world database as a condition of EAP approval.

Impact of regional differences and neighborhood socioeconomic deprivation on the outcomes of patients with lower extremity wounds evaluated by a limb-preservation service.

OBJECTIVE: Management of lower extremity (LE) wounds has evolved with the establishment of specialized limb preservation services. Although clinical factors contribute to limb outcomes, socioeconomic status and community factors also influence the risk for limb loss. The Distressed Community Index (DCI) score is a validated index of social deprivation created to provide an objective measure of economic well-being in United States communities. Few studies have examined the influence of geographic deprivation on outcomes in patients with LE wounds. We examined relationships between socioeconomic deprivation and outcomes of inpatients evaluated by a dedicated limb preservation service (Functional Limb Extremity Service [FLEX]). METHODS: Inpatients referred to FLEX over a 5-year period were included. Wound, Ischemia, foot Infection (WIfI) staging was collected. DCI scores were determined using seven indices based on ZIP Code. Outcomes included any minor or major amputations, any endovascular or open LE revascularization, or wound care procedures. Disease etiology, demographic, and anthropometric data were collected. Associations between neighborhood deprivation and limb-specific outcomes were evaluated in models for the DCI and each of its components separately. RESULTS: A total of 677 patients were included. Thirty-eight percent were female, with a mean age of 64 years. Sixty percent had WIfI stage 3 or 4 risk of amputation, and 43% had WIfI stage 3 or 4 risk of revascularization. Mean ankle-brachial index and toe pressure were 0.96 (standard deviation [SD], 0.43) and 80 (SD, 57) mmHg. Thirty-five percent were non-White. Amputation was performed in 31% of patients, whereas 17% underwent revascularization. The mean distress score was 64 (SD, 24). Mean DCI scores did not differ across WIfI scores. Likewise, overall DCI distress score was not related to any of the outcomes in univariable or multivariable linear regression models. In univariable linear regression models for amputation, higher poverty rate (odds ratio for SD increase 1.20; 95% confidence interval, 1.02-1.42; P = .025) was significantly associated with the outcome. In multivariable models, neither DCI distress score nor any of its components remained significantly associated with the outcome. CONCLUSIONS: Despite known racial disparities in limb-specific outcomes, an aggregate measure of community level distress was not found to be related to outcomes. Although the poverty rate demonstrated a significant relationship with amputation in univariable analysis, this association was not found in multivariable models. Notably, non-White race emerged as a predictor of amputation, underscoring the importance of addressing racial disparities in LE outcomes. Further investigation of potential determinants of LE outcomes is needed, particularly the interaction of such factors with race.

MAIT cell-MR1 reactivity is highly conserved across multiple divergent species.

Mucosal-associated invariant T (MAIT) cells are a subset of unconventional T cells that recognize small molecule metabolites presented by major histocompatibility complex class I related protein 1 (MR1), via an αß T cell receptor (TCR). MAIT TCRs feature an essentially invariant TCR α-chain, which is highly conserved between mammals. Similarly, MR1 is the most highly conserved major histocompatibility complex-I-like molecule. This extreme conservation, including the mode of interaction between the MAIT TCR and MR1, has been shown to allow for species-mismatched reactivities unique in T cell biology, thereby allowing the use of selected species-mismatched MR1-antigen (MR1-Ag) tetramers in comparative immunology studies. However, the pattern of cross-reactivity of species-mismatched MR1-Ag tetramers in identifying MAIT cells in diverse species has not been formally assessed. We developed novel cattle and pig MR1-Ag tetramers and utilized these alongside previously developed human, mouse, and pig-tailed macaque MR1-Ag tetramers to characterize cross-species tetramer reactivities. MR1-Ag tetramers from each species identified T cell populations in distantly related species with specificity that was comparable to species-matched MR1-Ag tetramers. However, there were subtle differences in staining characteristics with practical implications for the accurate identification of MAIT cells. Pig MR1 is sufficiently conserved across species that pig MR1-Ag tetramers identified MAIT cells from the other species. However, MAIT cells in pigs were at the limits of phenotypic detection. In the absence of sheep MR1-Ag tetramers, a MAIT cell population in sheep blood was identified phenotypically, utilizing species-mismatched MR1-Ag tetramers. Collectively, our results validate the use and define the limitations of species-mismatched MR1-Ag tetramers in comparative immunology studies.

Precision off-the-shelf natural killer cell therapies for oncology with logic-gated gene circuits.

Acute myeloid leukemia (AML) is an aggressive disease with a poor prognosis (5-year survival rate of 30.5% in the United States). Designing cell therapies to target AML is challenging because no single tumor-associated antigen (TAA) is highly expressed on all cancer subpopulations. Furthermore, TAAs are also expressed on healthy cells, leading to toxicity risk. To address these targeting challenges, we engineer natural killer (NK) cells with a multi-input gene circuit consisting of chimeric antigen receptors (CARs) controlled by OR and NOT logic gates. The OR gate kills a range of AML cells from leukemic stem cells to blasts using a bivalent CAR targeting FLT3 and/or CD33. The NOT gate protects healthy hematopoietic stem cells (HSCs) using an inhibitory CAR targeting endomucin, a protective antigen unique to healthy HSCs. NK cells with the combined OR-NOT gene circuit kill multiple AML subtypes and protect primary HSCs, and the circuit also works in vivo.

Comparative transcriptional analysis identifies genes associated with the attenuation of Theileria parva infected cells after long-term in vitro culture.

Autologous administration of attenuated Theileria parva-infected cells induces immunity to T. parva in cattle. The mechanism of attenuation, however, is largely unknown. Here, we used RNA sequencing of pathogenic and attenuated T. parva-infected T-cells to elucidate the transcriptional changes underpinning attenuation. We observed differential expression of several host genes, including TRAIL, PD-1, TGF-ß and granzymes that are known to regulate inflammation and proliferation of infected cells. Importantly, many genes linked with the attenuation of the related T. annulata-infected cells were not dysregulated in this study. Furthermore, known T. parva antigens were not dysregulated in attenuated relative to pathogenic cells, indicating that attenuation is not due to enhanced immunogenicity. Overall this study suggests that attenuation is driven by a decrease in proliferation and restoration of the inflammatory profile of T. parva-infected cells. Additionally, it provides a foundation for future mechanistic studies of the attenuation phenotype in Theileria-infected cells.

Adapting a Financial Incentives Intervention for Smoking Cessation with Alaska Native Families: Phase 1 Qualitative Research to Inform the Aniqsaaq (To Breathe) Study.

INTRODUCTION: Alaska Native and American Indian (ANAI) peoples in Alaska currently experience a disproportionate burden of morbidity and mortality from tobacco cigarette use. Financial incentives for smoking cessation are evidence-based, but a family-level incentive structure has not been evaluated. We used a community-based participatory research and qualitative approach to culturally adapt a smoking cessation intervention with ANAI families. METHODS: We conducted individual, semi-structured telephone interviews with 12 ANAI adults who smoke, 12 adult family members, and 13 Alaska Tribal Health System stakeholders statewide between November 2022-March 2023. Through content analysis, we explored intervention receptivity, incentive preferences, culturally aligned recruitment and intervention messaging, and future implementation needs. RESULTS: Participants were receptive to the intervention. Involving a family member was viewed as novel and aligned with ANAI cultural values of commitment to community and familial interdependence. Major themes included choosing a family member who is supportive and understanding, keeping materials positive and encouraging, and offering cash and non-cash incentives for family members to choose (e.g., fuel, groceries, activities). Participants indicated that messaging should emphasize family collaboration and that cessation resources and support tips should be provided. Stakeholders also reinforced that program materials should encourage the use of other existing evidence-based cessation therapies (e.g., nicotine replacement, counseling). CONCLUSIONS: Adaptations, grounded in ANAI cultural strengths were made to the intervention and recruitment materials based on participant feedback. Next steps include a beta-test for feasibility and a randomized controlled trial for efficacy. IMPLICATIONS: This is the first study to design and adapt a financial incentives intervention promoting smoking cessation among Alaska Native or American Indian (ANAI) peoples and the first to involve the family system. Feedback from this formative work was used to develop a meaningful family-level incentive structure with ANAI people who smoke and family members and ensure intervention messaging is supportive and culturally aligned. The results provide qualitative knowledge that can inform future family-based interventions with ANAI communities, including our planned randomized controlled trial of the intervention.

Safety and complications of continuation of aspirin therapy in patients undergoing robot-assisted laparoscopic simple prostatectomy.

To evaluate the safety and feasibility of continued perioperative aspirin at the time of robotic assisted simple prostatectomy (RASP). We performed a retrospective review of our IRB approved institutional database of patients who underwent RASP between 2013 and 2022. Comparative groups included patients taking aspirin in the perioperative period and those not taking aspirin pre-operatively. The primary outcome was any post-operative bleeding related complication using the modified Clavien-Dindo classification. Secondary outcomes included the identification of risk factors for increased blood loss in the entire study population, operative time, and blood transfusion requirement. 143 patients underwent RASP of which 55 (38.5%) patients continued perioperative aspirin therapy and 88 (61.5%) patients did not. Baseline demographics were similar between groups. Patients taking perioperative aspirin had a higher rate of hypertension (74.5% vs 58.0%, p = 0.04) and other cardiovascular disease (30.9% vs 11.4%, p = 0.007). Postoperative complications were similar between the groups (Clavien-Dindo ≥ 3; p = 0.43). Median blood loss (150 cc vs 150 cc, p = 0.38), percentage drop in hemoglobin (13.4 vs 13.2, p = 0.94) and blood transfusion rate (3.6 vs 1.1, p = 0.56) were also similar between groups. The median blood loss was 150 ml for the whole study population. On regression analysis, neither aspirin nor any other variable was associated with increased blood loss (> 150 ml). Aspirin can be safely continued perioperatively in patients undergoing RASP without any risk of bleeding related complications, blood loss, or increased transfusion rate.

Human Action Recognition and Note Recognition: A Deep Learning Approach Using STA-GCN.

Human action recognition (HAR) is growing in machine learning with a wide range of applications. One challenging aspect of HAR is recognizing human actions while playing music, further complicated by the need to recognize the musical notes being played. This paper proposes a deep learning-based method for simultaneous HAR and musical note recognition in music performances. We conducted experiments on Morin khuur performances, a traditional Mongolian instrument. The proposed method consists of two stages. First, we created a new dataset of Morin khuur performances. We used motion capture systems and depth sensors to collect data that includes hand keypoints, instrument segmentation information, and detailed movement information. We then analyzed RGB images, depth images, and motion data to determine which type of data provides the most valuable features for recognizing actions and notes in music performances. The second stage utilizes a Spatial Temporal Attention Graph Convolutional Network (STA-GCN) to recognize musical notes as continuous gestures. The STA-GCN model is designed to learn the relationships between hand keypoints and instrument segmentation information, which are crucial for accurate recognition. Evaluation on our dataset demonstrates that our model outperforms the traditional ST-GCN model, achieving an accuracy of 81.4%.